Seagers makes it three in row for new manager.
A gift-wrapped early goal from Seager and a late penalty by the same player were enough to give Tudno the points.
In between, Port dominated possession and the territory but failed to turn these advantages into goalscoring chances.
The home team were on the attack from the start, but out of the blue disaster struck for the Traeth men after nine minutes.
Under no apparent pressure Grahame Austin missed his kick on the edge of the box and allowed the ball to roll kindly for Seager, who was free to pounce goalwards, netting past the advancing Richard Harvey.
After 20 minutes Port drew level when Leon Newell did well to control a long cross-field pass, cut inside to find Grahame Boylan in the box with a low ball, and the striker''s perfect assist saw Dan Pyrs net with a low shot from 10 yards.
Port controlled the rest of the half, but the heroics of Tudno keeper Andy Metcalf denied Scott Sephton and Newell.
The home team continued to apply all the pressure after the restart, but again Metcalf did well to keep out Sephton''s well-struck shot.
Gradually with Port, despite their domination, failing to find a winner the visitors began to mount a few attacks of their own with Lee Thomas and Seager prominent.
With less than 10 minutes left a melee in the Porthmadog box ended with referee Scott Langley showing Austin a yellow card and pointing to the spot.
Seager coolly dispatched the penalty which sealed three crucial points.